The establishment and maintenance of epigenetic profiles play an important role in the regulation of gene expression in development, physiology, and diseases. Our proposal focuses on understanding how promoter and enhancer histone marks influence nucleosome positioning in vivo, and how in turn they are influenced by transcription. The model organism zebrafish is a unique vertebrate system to address these questions. Before the maternal-zygotic transition (MZT), the genome of early zebrafish embryos is not transcribed and is not occupied by histone marks such as H3K4me3 or H3K27me3. This system therefore allows the study of the transition from a non-transcribed to a transcribed genome. Moreover, large numbers of stage-synchronized embryos can be collected for genomics experiments. We propose to use RNA-seq, Pol II and histone mark ChIP-seq, and nucleosome-seq before, during, and after the onset of transcription during zebrafish MZT to answer the following questions: (1) which genes are maternally loaded versus zygotically expressed in zebrafish early embryonic development? (2) when are different histone marks established at different promoters and enhancers, how are promoter and enhancer marks related and how are they related to the presence of maternally loaded versus zygotically expressed transcription factors? (3) What is the effect of intrinsic DNA sequence, histone mark establishment, Pol II binding, transcription initiation and elongation on nucleosome positioning in vivo? Collectively, the project will provide insights into the interrelationship between gene regulation and the establishment and maintenance of epigenetic profiles in embryonic development.